A novel methodology has been developed for the investigation of bacterial spores. Specifically, this method has been used to probe the spore coat composition of several Bacillus species. This technique may be useful in many applications; most notably, development of novel detection schemes toward potentially harmful biological agents. This method would also be useful as an ancillary environmental monitoring system where sterility is of importance (i.e., food preparation areas as well as invasive and minimally invasive medical applications). This unique detection scheme is based on the near-infrared (NIR) Surface-Enhanced-Raman-Scattering (SERS) from single, optically trapped, bacterial spores. The SERS spectra of several bacterial spores in aqueous media have been measured using SERS substrates based on 60-nm diameter gold colloids bound to 3-Aminopropyltriethoxysilane derivatized glass. The light from a 785-nm laser diode was used to capture/manipulate as well as simultaneously excite the SERS of an individual bacterial spore. The collected SERS spectra were examined for uniqueness and the applicability of this technique for the species identification of bacterial spores.